Validation of the Cepheid Xpert® Xpress SARS-CoV-2 using upper and lower respiratory tract specimens

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Abstract

This study validated the performance of the reverse transcriptase‐polymerase chain reaction (rRT-PCR) based Cepheid Xpert® Xpress SARS-CoV-2 assay against the TIB MOLBIOL E-gene/EAV, a standard laboratory rRT-PCR SARS-CoV-2 assay. Upper and lower respiratory tract samples (nasopharyngeal and nasal swabs, bronchoalveolar lavage, and tracheal aspirate) were obtained from patients suspected to have contracted COVID-19. Results from the Xpert® Xpress and standard rRT-PCR assays were compared for positive and negative agreement and analyzed for precision, reproducibility, 95% confidence intervals, and coefficients of variation. The Xpert® Xpress assay demonstrated 100% agreement with the standard lab rRT-PCR for both upper and lower respiratory tract samples. Both the Xpert® Xpress and lab rRT-CPR identified weakly positive (Ct values 35–39) sample replicates with 100% reproducibility and showed 100% precision in identifying triplicates of upper respiratory tract samples. The single-cartridge Xpert® Xpress system has a short turnaround time and can be employed to improve patient management and hospital bed allocation. Further verification of the system is required before implementation and consideration must be paid to its higher cost and impracticality for high-throughput use.

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Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR

Victor M Corman, Olfert Landt, Marco Kaiser … (2020)

Background The ongoing outbreak of the recently emerged novel coronavirus (2019-nCoV) poses a challenge for public health laboratories as virus isolates are unavailable while there is growing evidence that the outbreak is more widespread than initially thought, and international spread through travellers does already occur. Aim We aimed to develop and deploy robust diagnostic methodology for use in public health laboratory settings without having virus material available. Methods Here we present a validated diagnostic workflow for 2019-nCoV, its design relying on close genetic relatedness of 2019-nCoV with SARS coronavirus, making use of synthetic nucleic acid technology. Results The workflow reliably detects 2019-nCoV, and further discriminates 2019-nCoV from SARS-CoV. Through coordination between academic and public laboratories, we confirmed assay exclusivity based on 297 original clinical specimens containing a full spectrum of human respiratory viruses. Control material is made available through European Virus Archive – Global (EVAg), a European Union infrastructure project. Conclusion The present study demonstrates the enormous response capacity achieved through coordination of academic and public laboratories in national and European research networks.

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Detection of SARS-CoV-2 by Use of the Cepheid Xpert Xpress SARS-CoV-2 and Roche cobas SARS-CoV-2 Assays

Angelica Moran, Kathleen G Beavis, Scott Matushek … (2020)

LETTER Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a novel coronavirus responsible for a December 2019 outbreak in Wuhan, China, causes a syndrome characterized by fever, cough, and dyspnea progressing to acute respiratory distress syndrome (1). SARS-CoV-2 quickly spread to other countries, with the new coronavirus disease 2019 (COVID-19) declared a pandemic in March 2020 (2 – 4). Rapid testing for SARS-CoV-2 is important for epidemiological tracking and institution of quarantine procedures (5). The clinical description of COVID-19 continues to evolve; with transmission by asymptomatic individuals reported (6 – 8), widespread testing is necessary. Multiple reverse transcription-PCR (RT-PCR) assays have received emergency use authorization from the U.S. Food and Drug Administration. The Roche cobas SARS-CoV-2 assay is a qualitative test that detects SARS-CoV-2-specific ORF1 and part of the E gene, conserved across sarbecoviruses, including SARS-CoV-2 (9). The Cepheid Xpert Xpress SARS-CoV-2 assay also detects the pan-sarbecovirus E gene but detects the N2 region of the N gene as its SARS-CoV-2-specific target (10). This report compares results from specimens tested with both assays. Eight nasal and 95 nasopharyngeal specimens were collected from inpatients and ambulatory patients at the University of Chicago. Samples were tested by the Roche cobas SARS-CoV-2 assay on the cobas 6800 system (Roche Molecular Systems, Branchburg, NJ) and by the Cepheid Xpert Xpress SARS-CoV-2 assay on the GeneXpert system (Cepheid, Sunnyvale, CA). Of these 103 specimens, 42 tested positive and 60 tested negative with both systems, for an agreement of 99%. Testing was repeated on the single specimen with discrepant results. For this specimen, the Roche assay was repeatedly negative for SARS-CoV-2. The initial Cepheid assay result was positive for SARS-CoV-2, though the cycle threshold (CT ) values for detection of the E gene were 0.0 (negative) and 42.0 (low positivity) for the N gene. Repeat Cepheid testing was negative for both targets. These results suggest that SARS-CoV-2 was present at a very low concentration, near the detection limit of the Cepheid assay. For the 42 positive samples, CT values for the E gene ranged from 15.05 to 39.75 (mean, 26.35; standard deviation [SD], 6.69) for the Roche assay and 13.6 to 38.2 (mean, 24.8; SD, 7.1) for the Cepheid assay. By Bland-Altman analysis to assess agreement, CT values were lower in the Cepheid assay for 37 of 42 samples (mean difference, –1.57; 95% limits of agreement, –5.34, 2.20). This might be due to differences in primer sequences for the E gene, reagents, or amplification conditions. Limitations of this study include the small sample size of SARS-CoV-2-positive specimens, as testing was limited to patients within our institution. The assays also detect different SARS-CoV-2-specific genes, which may lead to false-negative results if a mutation prevents primer binding. The Cepheid assay is a 45-min random-access assay, with throughput dependent on the number of instrument slots. The Roche platform is batch based, accommodating 90 samples/run every 90 min. As each run requires up to 3 h and 45 min, throughput is approximately 1 result per minute. Overall, the Cepheid Xpert Xpress SARS-CoV-2 and Roche cobas SARS-CoV-2 assays show excellent agreement (>99%), and their combined usage can be tailored to maximize SARS-CoV-2 testing.

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Brief validation of the novel GeneXpert Xpress SARS-CoV-2 PCR assay

Daniel Goldenberger, Karoline Leuzinger, Kirstine K. Sogaard … (2020)

The clinical and epidemiologic management of the SARS-CoV-2 pandemic is critically dependent on molecular assays with short turn-around time. We validated the novel Xpert Xpress SARS-CoV-2 assay using a commercial nucleic acid testing (Roche Cobas 6800). We found an excellent concordance over a range of SARS-CoV-2 loads and across established human coronaviruses.

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Author and article information

Contributors

Kassie Rong:

ORCID: 0000-0001-8962-1492

Journal

Journal ID (publisher-id): 1886

Title: European Journal of Microbiology and Immunology

Abbreviated Title: EuJMI

Publisher: Akadémiai Kiadó (Budapest )

ISSN (Print): 2062-509X

ISSN (Electronic): 2062-8633

Publication date (Electronic): 14 March 2022

Publication date (Print): 20 April 2022

Volume: 12

Issue: 1

Pages: 18-21

Affiliations

[1 ] Western University, Department of Physiology and Pharmacology , London, ON, Canada

[2 ] Western University, Department of Pathology and Laboratory Medicine , London, ON, Canada

[3 ] London Health Sciences Centre , London, ON, Canada

Author notes

[* ]Corresponding author. E-mail: krong3@ 123456uwo.ca

Author information

Kassie Rong https://orcid.org/0000-0001-8962-1492

Article

DOI: 10.1556/1886.2022.00003

PMC ID: 9036648

PubMed ID: 35286278

SO-VID: 2eca142b-d524-4134-aecd-6d936e1d2f1e

License:

Open Access. This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 International License ( https://creativecommons.org/licenses/by-nc/4.0/), which permits unrestricted use, distribution, and reproduction in any medium for non-commercial purposes, provided the original author and source are credited, a link to the CC License is provided, and changes – if any – are indicated.

History

Date received : 02 February 2022

Date accepted : 27 February 2022

Page count

Tables: 3, Equations: 0, References: 6, Pages: 04

ScienceOpen disciplines: Medicine,Immunology,Health & Social care,Microbiology & Virology,Infectious disease & Microbiology

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Validation of the Cepheid Xpert® Xpress SARS-CoV-2 using upper and lower respiratory tract specimens

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